Atomic resolution crystallography reveals how changes in pH shape the protein microenvironment

Nature Chemical Biology

Volumn 2, Issue 5, 2006, Pages 259-264

  Lyubimov, Artem Y ^a   Lario, Paula I ^a   Moustafa, Ibrahim ^a   Vrielink, Alice ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONYL DERIVATIVE; CHOLESTEROL OXIDASE; FLAVOPROTEIN; HYDROGEN; OXIDOREDUCTASE; QUERCETIN;

ARTICLE; CATALYSIS; CRYSTALLOGRAPHY; MICROENVIRONMENT; OXIDATION; OXIDATION REDUCTION REACTION; PH; PRIORITY JOURNAL; STREPTOMYCES;

STREPTOMYCES; STREPTOMYCES SP.;

EID: 33646457379     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio784     Document Type: Article

References (32)

1. Mirsky, A.E. & Pauling, L. On the structure of native, denatured, and coagulated proteins. Proc. Natl. Acad. Sci. USA 22, 439-447 (1936).
2. Pace, C.N., Shirley, B.A., McNutt, M. & Gajiwala, K. Forces contributing to the conformational stability of proteins. FASEB J. 10, 75-83 (1996).
3. Pace, C.N. Polar group burial contributes more to protein stability than nonpolar group burial. Biochemistry 40, 310-313 (2001).
4. Cleland, W.W. Low-barrier hydrogen bonds and enzymatic catalysis. Arch. Biochem. Biophys. 382, 1-5 (2000).
5. Longhi, S., Czjzek, M., Lamzin, V., Nicolas, A. & Cambillau, C. Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis. J. Mol. Biol. 268, 779-799 (1997).
6. Kuhn, P. et al. The 0.78 A structure of a serine protease: Bacillus lentus subtilisin. Biochemistry 37, 13446-13452 (1998).
7. Katona, G. et al. X-ray structure of a serine protease acyl-enzyme complex at 0.95-A resolution. J. Biol. Chem. 277, 21962-21970 (2002).
8. Berisio, R. et al. Protein titration in the crystal state. J. Mol. Biol. 292, 845-854 (1999).
9. Lario, P.I., Sampson, N. & Vrielink, A. Sub-atomic resolution crystal structure of cholesterol oxidase: what atomic resolution crystallography reveals about enzyme mechanism and the role of the FAD cofactor in redox activity. J. Mol. Biol. 326, 1635-1650 (2003).
10. Dunlop, K.V., Irvin, R.T. & Hazes, B. Pros and cons of cryocrystallography: should we also collect a room-temperature data set? Acta Crystallogr. D Biol. Crystallogr. 61, 80-87 (2005).
11. Sampson, N.S. & Vrielink, A. Cholesterol oxidases: a study of nature's approach to protein design. Acc. Chem. Res. 36, 713-722 (2003).
12. Kass, I.J. & Sampson, N.S. Evaluation of the role of His447 in the reaction catalyzed by cholesterol oxidase. Biochemistry 37, 17990-18000 (1998).
13. Yin, Y. Functional studies to probe the active site structure of cholesterol oxidase. PhD Thesis, Department of Chemistry, State Univ. of New York, Stony Brook, New York, USA, 2002.
14. Hall, L.H., Orchard, B.J. & Tripathy, S.K. The structure and properties of flavins: molecular orbital study based on totally optimized geometries. II. Molecular orbital structure and electron distribution. Int. J. Quantum Chem. 31, 217-242 (1987).
15. Massey, V. & Ganther, H. On the interpretation of the absorption spectra of flavoproteins with special reference to D-amino acid oxidase. Biochemistry 4, 1161-1173 (1965).
16. Sheldrick, G.M. & Schneider, T.R. SHELXL: High-resolution refinement. in Methods in Enzymology (eds. Carter, C.W.J. & Sweet, R.M.) 319-343 (Academic Press, Boston, 1997).
17. Ondrechen, M.J., Clifton, J.G. & Ringe, D. THEMATICS: a simple computational predictor of enzyme function from structure. Proc. Natl. Acad. Sci. USA 98, 12473-12478 (2001).
18. Ko, J. et al. Statistical criteria for the identification of protein active sites using Theoretical Microscopic Titration Curves. Proteins 59, 183-195 (2005).
19. Hall, L.H., Orchard, B.J. & Tripathy, S.K. The structure and properties of flavins: molecular orbital study based on totally optimized geometries. I. Molecular geometry investigations. Int. J. Quantum Chem. 31, 195-216 (1987).
20. Hall, L.H., Bowers, M.L. & Durfor, C.N. Further consideration of flavin coenzyme biochemistry afforded by geometry-optimized molecular orbital calculations. Biochemistry 26, 7401-7409 (1987).
21. Li, H., Robertson, A.D. & Jensen, J.H. Very fast empirical prediction and rationalization of protein pKa values. Proteins 61, 704-721 (2005).
22. Bruice, T.C. & Schmir, G.L. Imidazole catalysis. II. The reaction of substituted imidazoles with phenyl acetates in aqueous solution. J. Am. Chem. Soc. 80, 148-156 (1958).
23. Yue, Q.K., Kass, I.J., Sampson, N.S. & Vrielink, A. Crystal structure determination of cholesterol oxidase from Streptomyces and structural characterization of key active site mutants. Biochemistry 38, 4277-4286 (1999).
24. Engh, R.A. & Huber, R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A 47, 392-400 (1991).
25. McRee, D.E. XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156-165 (1999).
26. Vaguine, A.A., Richelle, J. & Wodak, S.J. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr. D Biol. Crystallogr. 55, 191-205 (1999).
27. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291 (1993).
28. Berman, H.M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000).
29. Kleywegt, G.J. & Jones, TA. xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Crystallogr. D Biol. Crystallogr. 52, 826-828 (1996).
30. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132 (2004).
31. DeLano, W.L. The PyMOL molecular graphics system. (DeLano Scientific, San Carlos, California, USA, 2002). (http://www.pymol.org).
32. Collaborative Computational Project. N. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-763 (1994).